Optical mapping by low-cost instrumentation and disposable chemically induced nanochannels

The cost of fabrication and instrumentation presents a significant barrier to uptake of optical mapping as a tool for genomic investigation. Here a low cost optical instrumentation system to perform optical genomic mapping of DNA fragment restriction digestion by nanochannel confinement is presented. Specifically, the system is used for the detection of YOYO-1 labeled DNA within chemically formed nanochannels on a polystyrene chip. The formation of nanochannels on the polystyrene chip is achieved by solvent swelling of an injection moulded polystyrene substrate. The inverted microscope based system is compact and of low-cost but offers the sensitivity to detect individual fragments ranging from 0.56Kb to 9.4Kb of the lambda-phage genome within a channels. Conformation of DNA within nanochannels driven by capillary flow is most consistent with modeled polymer extension in nanoslit.